6MF0

Crystal Structure Determination of Human/Porcine Chimera Coagulation Factor VIII

• PDB DOI: https://doi.org/10.2210/pdb6MF0/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Sus scrofa, Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2018-09-07 Released: 2019-09-11 
• Deposition Author(s): Smith, I.W., Spiegel, P.C.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.287 
• R-Value Work: 0.206 
• R-Value Observed: 0.210 

Literature

The 3.2 angstrom structure of a bioengineered variant of blood coagulation factor VIII indicates two conformations of the C2 domain.

Smith, I.W., d'Aquino, A.E., Coyle, C.W., Fedanov, A., Parker, E.T., Denning, G., Spencer, H.T., Lollar, P., Doering, C.B., Spiegel Jr., P.C.

(2020) J Thromb Haemost 18: 57-69

• PubMed: 31454152 
• DOI: https://doi.org/10.1111/jth.14621
• Primary Citation of Related Structures:  
  6MF0, 6MF2


• PubMed Abstract: 
  

  Coagulation factor VIII represents one of the oldest protein-based therapeutics, serving as an effective hemophilia A treatment for half a century. Optimal treatment consists of repeated intravenous infusions of blood coagulation factor VIII (FVIII) per week for life. Despite overall treatment success, significant limitations remain, including treatment invasiveness, duration, immunogenicity, and cost. These issues have inspired research into the development of bioengineered FVIII products and gene therapies.

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Organizational Affiliation: 

Department of Chemistry, Western Washington University, Bellingham, Washington.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 342.56 kDa 
• Atom Count: 20,622 
• Modelled Residue Count: 2,503 
• Deposited Residue Count: 2,934 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VIII chimera	A, B	1,467	Sus scrofa, Homo sapiens	Mutation(s): 0  Gene Names: F8, CF8, F8C Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P12263 (Sus scrofa) Explore P12263  Go to UniProtKB:  P12263
Find proteins for P00451 (Homo sapiens) Explore P00451  Go to UniProtKB:  P00451
PHAROS:  P00451 GTEx:  ENSG00000185010
UniProt Groups	P12263P00451

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E, F	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G35459KZ GlyCosmos:  G35459KZ GlyGen:  G35459KZ

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC GlyCosmos:  G56014GC GlyGen:  G56014GC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	J [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU1	K [auth A], N [auth B]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N
CA	I [auth A], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.287 
• R-Value Work: 0.206 
• R-Value Observed: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.005	α = 90
b = 135.863	β = 90.151
c = 196.107	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Currently 6MF0 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Smith, I.W., Spiegel, P.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R15 HL103518
National Science Foundation (NSF, United States)	United States	MRI 1429164

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2020-01-15
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary